RetrogeneDB ID: retro_cjac_507

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:15913294..15913620(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ARF4
• Ensembl ID: ENSCJAG00000019922
• Aliases: None
• Description: ADP-ribosylation factor 4 [Source:HGNC Symbol;Acc:655]

Sequence

>retro_cjac_507
GGGGAGACAGTCACCACCATTCCTACCATTGGCTGAAACATGGAAGCAGTAGACCGTACGAACATTTGGTTCACAGTATG
GGATGGGGGGTCAAGACAGAATTAGCCCTCTCTGATAGTATTACTTCCGAAATACCCAACGTCTTCTTTTTGTGGTAGAC
AGCGATCGTCGTGAAAGAATTAAGGAGGTAGCAGGTGAGCTGCAGACTGCTTCTGGAGACCAGTTGAGAGAGGCAGTGAT
GCTGCTTTTTGAAAACTGCAGGATTTGCCAAAAGCTCTTCGATCTCTTCCTAACAGGACATGGTCTGTTCAAGCCACATG
CGTAAC

Alignment

ORF - retro_cjac_507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.65 %
• Parental protein coverage: 61.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GEIVTTIPTIGFNVETVEYKNICFTVWDVGG-QDRIRPLWKHYFQNTQGLIFVVDSNDRERIQEVADELQ
          GE.VTTIPTIG.N.E.V...NI.FTVWD.GG.QDRI.PL...YF.NTQ.L.FVVDS..RERI.EVA.ELQ
Retrocopy GETVTTIPTIG*NMEAVDRTNIWFTVWD-GG>QDRISPL**YYFRNTQRLLFVVDSDRRERIKEVAGELQ

Parental  KMLLVDELRDAVLLLFAN-KQDLPNAM-AISEMTDKLGLQSLRN
          .....D.LR.AV.LLF.N..QDLP.A...IS...D.......RN
Retrocopy -TASGDQLREAVMLLFEN<LQDLPKAL<SISS*QDMVCSSHMRN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	82.91 RPM
SRP051959_heart	0.00 RPM	30.40 RPM
SRP051959_kidney	0.00 RPM	51.69 RPM
SRP051959_liver	0.04 RPM	85.43 RPM
SRP051959_lung	0.02 RPM	41.38 RPM
SRP051959_lymph_node	0.00 RPM	37.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.70 RPM
SRP051959_spleen	0.11 RPM	48.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_507 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_507 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1296
Pan troglodytes	retro_ptro_888
Gorilla gorilla	retro_ggor_1016
Pongo abelii	retro_pabe_1075

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016069	1 retrocopy	retro_btau_542,
Choloepus hoffmanni	ENSCHOG00000006427	4 retrocopies	retro_chof_1024, retro_chof_1807, retro_chof_2368, retro_chof_36,
Ciona intestinalis	ENSCING00000021790	1 retrocopy	retro_cint_10,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120, retro_cjac_470,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Callithrix jacchus	ENSCJAG00000019922	1 retrocopy	retro_cjac_507 ,
Cavia porcellus	ENSCPOG00000010334	1 retrocopy	retro_cpor_1261,
Dipodomys ordii	ENSDORG00000004312	1 retrocopy	retro_dord_731,
Homo sapiens	ENSG00000168374	2 retrocopies	retro_hsap_1296, retro_hsap_4221,
Gorilla gorilla	ENSGGOG00000000294	1 retrocopy	retro_ggor_1552,
Microcebus murinus	ENSMICG00000002015	3 retrocopies	retro_mmur_1528, retro_mmur_1558, retro_mmur_360,
Myotis lucifugus	ENSMLUG00000007990	1 retrocopy	retro_mluc_2272,
Macaca mulatta	ENSMMUG00000018617	1 retrocopy	retro_mmul_50,
Monodelphis domestica	ENSMODG00000000185	1 retrocopy	retro_mdom_1538,
Nomascus leucogenys	ENSNLEG00000007270	3 retrocopies	retro_nleu_2106, retro_nleu_2703, retro_nleu_2704,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Otolemur garnettii	ENSOGAG00000012034	4 retrocopies	retro_ogar_1407, retro_ogar_1501, retro_ogar_2963, retro_ogar_764,
Pongo abelii	ENSPPYG00000013768	3 retrocopies	retro_pabe_1013, retro_pabe_1075, retro_pabe_3451,
Pan troglodytes	ENSPTRG00000015051	2 retrocopies	retro_ptro_2866, retro_ptro_888,
Rattus norvegicus	ENSRNOG00000012623	2 retrocopies	retro_rnor_1036, retro_rnor_1884,
Sorex araneus	ENSSARG00000009272	1 retrocopy	retro_sara_681,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614,
Tupaia belangeri	ENSTBEG00000007415	1 retrocopy	retro_tbel_2075,
Tarsius syrichta	ENSTSYG00000009748	1 retrocopy	retro_tsyr_2059,
Tursiops truncatus	ENSTTRG00000015381	1 retrocopy	retro_ttru_284,
Vicugna pacos	ENSVPAG00000003891	1 retrocopy	retro_vpac_459,